Research workbench
Three dimensional structure of broadly neutralizing anti - hepatitis C virus (HCV) glycoprotein E2 single chain fv fragment 1:7
Analyse Three dimensional structure of broadly neutralizing anti - hepatitis C virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U6R
- Type
- protein
- Length
- 463 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 1:7 (heavy chain); Antibody 1:7 (light chain)
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 1:7 (heavy chain) | protein | 126 | 5% helix, 52% strand | — |
| L, B | Antibody 1:7 (light chain) | protein | 105 | 3% helix, 52% strand | — |
| A | Antibody 1:7 (heavy chain) | protein | 127 | 5% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.76 | 0.79 | 66 | empty |
| 2 | 353 | 0.58 | 0.76 | 32 | empty |
| 3 | 292 | 0.56 | 0.76 | 28 | empty |
| 4 | 90 | 0.34 | 0.74 | 15 | empty |
| 5 | 55 | 0.28 | 0.75 | 12 | empty |
Interfaces
5 interfaces between chains.
- H–L · 931 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 823 Ų buried · 11 hydrogen bonds · protein-protein
- H–B · 339 Ų buried · 4 hydrogen bonds · protein-protein
- L–A · 326 Ų buried · 2 hydrogen bonds · protein-protein
- L–B · 93 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3U6R · Three dimensional structure of broadly neutralizing anti - Hepatitis C virus (HCV)… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3U6R · PDBe 3U6R
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